log "github.com/sirupsen/logrus"
)
-type exportHGVS struct {
+type outputFormat struct {
+ Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
+ PadLeft bool
}
-func (cmd *exportHGVS) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+var (
+ outputFormats = map[string]outputFormat{
+ "hgvs": outputFormatHGVS,
+ "vcf": outputFormatVCF,
+ }
+ outputFormatHGVS = outputFormat{Print: printHGVS}
+ outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
+)
+
+type exporter struct {
+ outputFormat outputFormat
+}
+
+func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
var err error
defer func() {
if err != nil {
priority := flags.Int("priority", 500, "container request priority")
refname := flags.String("ref", "", "reference genome `name`")
inputFilename := flags.String("i", "-", "input `file` (library)")
- outputFilename := flags.String("o", "-", "fasta output `file`")
+ outputFilename := flags.String("o", "-", "output `file`")
+ outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
pick := flags.String("pick", "", "`name` of single genome to export")
err = flags.Parse(args)
if err == flag.ErrHelp {
return 2
}
+ if f, ok := outputFormats[*outputFormatStr]; !ok {
+ err = fmt.Errorf("invalid output format %q", *outputFormatStr)
+ return 2
+ } else {
+ cmd.outputFormat = f
+ }
+
if *pprof != "" {
go func() {
log.Println(http.ListenAndServe(*pprof, nil))
return 1
}
runner := arvadosContainerRunner{
- Name: "lightning export-hgvs",
+ Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
RAM: 128000000000,
if err != nil {
return 1
}
- runner.Args = []string{"export-hgvs", "-local=true", "-pick", *pick, "-ref", *refname, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
+ runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
var output string
output, err = runner.Run()
if err != nil {
return 0
}
-func (cmd *exportHGVS) export(out io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
+func (cmd *exporter) export(out io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
need := map[tileLibRef]bool{}
var seqnames []string
for seqname, librefs := range refseq {
seqnames = append(seqnames, seqname)
for _, libref := range librefs {
- need[libref] = true
+ if libref.Variant != 0 {
+ need[libref] = true
+ }
}
}
sort.Strings(seqnames)
}
vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
for _, v := range vars {
+ if cmd.outputFormat.PadLeft {
+ v = v.PadLeft()
+ }
v.Position += refpos
log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String())
varslice := variantAt[v.Position]
if varslice == nil {
varslice = make([]hgvs.Variant, len(cgs)*2)
+ variantAt[v.Position] = varslice
}
varslice[cgidx*2+phase] = v
- variantAt[v.Position] = varslice
}
}
}
varslice[i].Position = pos
}
}
- for i := 0; i < len(cgs); i++ {
- if i > 0 {
- out.Write([]byte{'\t'})
- }
- var1, var2 := varslice[i*2], varslice[i*2+1]
- if var1.Position == 0 && var2.Position == 0 {
- out.Write([]byte{'.'})
- } else if var1 == var2 {
- fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
- } else {
- if var1.Position == 0 {
- var1.Position = pos
- }
- if var2.Position == 0 {
- var2.Position = pos
- }
- fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
- }
- }
- out.Write([]byte{'\n'})
+ cmd.outputFormat.Print(out, seqname, varslice)
}
}
}
return nil
}
+
+func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
+ refs := map[string]map[string]int{}
+ for _, v := range varslice {
+ if v.Ref == "" && v.New == "" {
+ continue
+ }
+ alts := refs[v.Ref]
+ if alts == nil {
+ alts = map[string]int{}
+ refs[v.Ref] = alts
+ }
+ alts[v.New] = 0
+ }
+ for ref, alts := range refs {
+ var altslice []string
+ for alt := range alts {
+ altslice = append(altslice, alt)
+ }
+ sort.Strings(altslice)
+ for i, a := range altslice {
+ alts[a] = i + 1
+ }
+ fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
+ for i := 0; i < len(varslice)/2; i++ {
+ v1, v2 := varslice[i*2], varslice[i*2+1]
+ a1, a2 := alts[v1.New], alts[v2.New]
+ if v1.Ref != ref {
+ a1 = 0
+ }
+ if v2.Ref != ref {
+ a2 = 0
+ }
+ fmt.Fprintf(out, "\t%d/%d", a1, a2)
+ }
+ out.Write([]byte{'\n'})
+ }
+}
+
+func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
+ for i := 0; i < len(varslice)/2; i++ {
+ if i > 0 {
+ out.Write([]byte{'\t'})
+ }
+ var1, var2 := varslice[i*2], varslice[i*2+1]
+ if var1 == var2 {
+ if var1.Ref == var1.New {
+ out.Write([]byte{'.'})
+ } else {
+ fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
+ }
+ } else {
+ fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
+ }
+ }
+ out.Write([]byte{'\n'})
+}
c.Check(ioutil.WriteFile(tmpdir+"/merged.gob", merged.Bytes(), 0666), check.IsNil)
hgvsout := &bytes.Buffer{}
- code = (&exportHGVS{}).RunCommand("lightning export-hgvs", []string{"-local", "-ref", "testdata/ref.fasta", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), hgvsout, os.Stderr)
+ code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), hgvsout, os.Stderr)
c.Check(code, check.Equals, 0)
c.Check(hgvsout.Len() > 0, check.Equals, true)
c.Logf("%s", hgvsout.String())
chr2:g.[887C>A];[887=]
chr2:g.[1042_1044del];[1042=]
chr2:g.[1043=];[1043_1044delinsAA]
+`)
+
+ vcfout := &bytes.Buffer{}
+ code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "vcf", "-i", tmpdir + "/merged.gob"}, bytes.NewReader(nil), vcfout, os.Stderr)
+ c.Check(code, check.Equals, 0)
+ c.Check(vcfout.Len() > 0, check.Equals, true)
+ c.Logf("%s", vcfout.String())
+ c.Check(vcfout.String(), check.Equals, `chr1 41 TT AA 1/0
+chr1 161 A T 0/1
+chr1 178 A T 0/1
+chr1 221 TCCA T 1/1
+chr1 302 TTTT AAAA 0/1
+chr2 812 ATTTTTCTTGCTCTC A 1/0
+chr2 830 CCTTGTATTTTT AA 1/0
+chr2 887 C A 1/0
+chr2 1041 GTGG G 1/0
+chr2 1043 GG AA 0/1
`)
}
projects / lightning.git / commitdiff